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Detailed information for vg0512682109:

Variant ID: vg0512682109 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 12682109
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CAACGGGAAGATTGCAGTAACCAAGCAACGGTGGCTGGTATCAAAACATGAGAAACACCCAAGCTGCACGAGATCATAAGAAAGTAAAAATAAGTACACC[C/A]
AACCATGAGCAGCTAATTAGTACTAAGGGGACGATATCATGTTTCACACACAACAGGGGTGCACCAAACCCATCCAGCATATTGGACCTAAGTTTTCCAC

Reverse complement sequence

GTGGAAAACTTAGGTCCAATATGCTGGATGGGTTTGGTGCACCCCTGTTGTGTGTGAAACATGATATCGTCCCCTTAGTACTAATTAGCTGCTCATGGTT[G/T]
GGTGTACTTATTTTTACTTTCTTATGATCTCGTGCAGCTTGGGTGTTTCTCATGTTTTGATACCAGCCACCGTTGCTTGGTTACTGCAATCTTCCCGTTG

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	95.10%	2.10%	2.77%	0.00%	NA
All Indica	2759	97.70%	0.00%	2.28%	0.00%	NA
All Japonica	1512	89.50%	6.30%	4.17%	0.00%	NA
Aus	269	99.60%	0.00%	0.37%	0.00%	NA
Indica I	595	95.50%	0.00%	4.54%	0.00%	NA
Indica II	465	96.60%	0.00%	3.44%	0.00%	NA
Indica III	913	99.80%	0.00%	0.22%	0.00%	NA
Indica Intermediate	786	97.70%	0.00%	2.29%	0.00%	NA
Temperate Japonica	767	90.50%	3.10%	6.39%	0.00%	NA
Tropical Japonica	504	90.30%	8.50%	1.19%	0.00%	NA
Japonica Intermediate	241	84.60%	12.00%	3.32%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	91.10%	4.40%	4.44%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0512682109	C -> A	LOC_Os05g22370.3	upstream_gene_variant ; 306.0bp to feature; MODIFIER	silent_mutation	Average:56.334; most accessible tissue: Zhenshan97 young leaf, score: 75.397	N	N	N	N
vg0512682109	C -> A	LOC_Os05g22370.2	intron_variant ; MODIFIER	silent_mutation	Average:56.334; most accessible tissue: Zhenshan97 young leaf, score: 75.397	N	N	N	N
vg0512682109	C -> A	LOC_Os05g22370.1	intron_variant ; MODIFIER	silent_mutation	Average:56.334; most accessible tissue: Zhenshan97 young leaf, score: 75.397	N	N	N	N
vg0512682109	C -> A	LOC_Os05g22370.4	intron_variant ; MODIFIER	silent_mutation	Average:56.334; most accessible tissue: Zhenshan97 young leaf, score: 75.397	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0512682109	1.01E-06	2.95E-07	mr1546_2	Jap_All	YES	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0512682109	NA	1.08E-06	mr1549_2	Jap_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251